The evaluation of activated sludge control strategies in wastewater treatment plants (WWTP) via mathematical modelling is a complex activity because several objectives; e.g. economic, environmental, technical and legal; must be taken into account at the same time, i.e. the evaluation of the alternatives is a multi-criteria problem. Activated sludge models are not well characterized and some of the parameters can present uncertainty, e.g. the influent fractions arriving to the facility and the effect of either temperature or toxic compounds on the kinetic parameters, having a strong influence in the model predictions used during the evaluation of the alternatives and affecting the resulting rank of preferences. Using a simplified version of the IWA Benchmark Simulation Model No. 2 as a case study, this article shows the variations in the decision making when the uncertainty in activated sludge model (ASM) parameters is either included or not during the evaluation of WWTP control strategies. This paper comprises two main sections. Firstly, there is the evaluation of six WWTP control strategies using multi-criteria decision analysis setting the ASM parameters at their default value. In the following section, the uncertainty is introduced, i.e. input uncertainty, which is characterized by probability distribution functions based on the available process knowledge. Next, Monte Carlo simulations are run to propagate input through the model and affect the different outcomes. Thus (i) the variation in the overall degree of satisfaction of the control objectives for the generated WWTP control strategies is quantified, (ii) the contributions of environmental, legal, technical and economic objectives to the existing variance are identified and finally (iii) the influence of the relative importance of the control objectives during the selection of alternatives is analyzed. The results show that the control strategies with an external carbon source reduce the output uncertainty in the criteria used to quantify the degree of satisfaction of environmental, technical and legal objectives, but increasing the economical costs and their variability as a trade-off. Also, it is shown how a preliminary selected alternative with cascade ammonium controller becomes less desirable when input uncertainty is included, having simpler alternatives more chance of success.